Section: Original Articles
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Journal Article

Enabling semantic queries across federated bioinformatics databases

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Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz
Database, Volume 2019, 2019, baz106, https://doi.org/10.1093/database/baz106
Published: 07 November 2019
Journal Article

Building an efficient curation workflow for the Arabidopsis literature corpus

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Donghui Li, Tanya Z. Berardini, Robert J. Muller, Eva Huala
Database, Volume 2012, 2012, bas047, https://doi.org/10.1093/database/bas047
Published: 06 December 2012
Journal Article

Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database

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Allan Peter Davis, Robin J. Johnson, Kelley Lennon-Hopkins, Daniela Sciaky, Michael C. Rosenstein, Thomas C. Wiegers, Carolyn J. Mattingly
Database, Volume 2012, 2012, bas051, https://doi.org/10.1093/database/bas051
Published: 06 December 2012
Journal Article

Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database

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Dina Vishnyakova, Emilie Pasche, Patrick Ruch
Database, Volume 2012, 2012, bas050, https://doi.org/10.1093/database/bas050
Published: 05 December 2012
Journal Article

The eFIP system for text mining of protein interaction networks of phosphorylated proteins

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Catalina O. Tudor, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
Database, Volume 2012, 2012, bas044, https://doi.org/10.1093/database/bas044
Published: 05 December 2012
Journal Article

Strategies for annotation and curation of translational databases: the eTUMOUR project

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Margarida Julià-Sapé, Miguel Lurgi, Mariola Mier, Francesc Estanyol, Xavier Rafael, Ana Paula Candiota, Anna Barceló, Alina García, M. Carmen Martínez-Bisbal, Rubén Ferrer-Luna, Àngel Moreno-Torres, Bernardo Celda, Carles Arús
Database, Volume 2012, 2012, bas035, https://doi.org/10.1093/database/bas035
Published: 22 November 2012
Journal Article

Collaborative biocuration—text-mining development task for document prioritization for curation

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Thomas C. Wiegers, Allan Peter Davis, Carolyn J. Mattingly
Database, Volume 2012, 2012, bas037, https://doi.org/10.1093/database/bas037
Published: 22 November 2012
Journal Article

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II

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Zhiyong Lu, Lynette Hirschman
Database, Volume 2012, 2012, bas043, https://doi.org/10.1093/database/bas043
Published: 15 November 2012
Journal Article

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

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Kimberly Van Auken, Petra Fey, Tanya Z. Berardini, Robert Dodson, Laurel Cooper, Donghui Li, Juancarlos Chan, Yuling Li, Siddhartha Basu, Hans-Michael Muller, Rex Chisholm, Eva Huala, Paul W. Sternberg, the WormBase Consortium
Database, Volume 2012, 2012, bas040, https://doi.org/10.1093/database/bas040
Published: 15 November 2012
Journal Article

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts

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Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu
Database, Volume 2012, 2012, bas041, https://doi.org/10.1093/database/bas041
Published: 15 November 2012
Journal Article

Developing a biocuration workflow for AgBase, a non-model organism database

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Lakshmi Pillai, Philippe Chouvarine, Catalina O. Tudor, Carl J. Schmidt, K. Vijay-Shanker, Fiona M. McCarthy
Database, Volume 2012, 2012, bas038, https://doi.org/10.1093/database/bas038
Published: 15 November 2012
Journal Article

Opportunities for text mining in the FlyBase genetic literature curation workflow

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Peter McQuilton, the FlyBase Consortium
Database, Volume 2012, 2012, bas039, https://doi.org/10.1093/database/bas039
Published: 15 November 2012
Journal Article

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

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Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur
Database, Volume 2012, 2012, bas042, https://doi.org/10.1093/database/bas042
Published: 15 November 2012
Journal Article

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database

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Harold J. Drabkin, Judith A. Blake, for the Mouse Genome Informatics Database
Database, Volume 2012, 2012, bas045, https://doi.org/10.1093/database/bas045
Published: 29 October 2012
Journal Article

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference

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Pascale Gaudet, Cecilia Arighi, Frederic Bastian, Alex Bateman, Judith A. Blake, Michael J. Cherry, Peter D’Eustachio, Robert Finn, Michelle Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica Munoz-Torres, Darren Natale, Claire O’Donovan, Francis Ouellette, Kim D. Pruitt … Raja Mazumder
Database, Volume 2012, 2012, bas036, https://doi.org/10.1093/database/bas036
Published: 29 October 2012
Journal Article

DFVF: database of fungal virulence factors

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Tao Lu, Bo Yao, Chi Zhang
Database, Volume 2012, 2012, bas032, https://doi.org/10.1093/database/bas032
Published: 22 October 2012
Journal Article

The Units Ontology: a tool for integrating units of measurement in science

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Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
Database, Volume 2012, 2012, bas033, https://doi.org/10.1093/database/bas033
Published: 05 October 2012
Journal Article

Assessment of community-submitted ontology annotations from a novel database-journal partnership

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Tanya Z. Berardini, Donghui Li, Robert Muller, Raymond Chetty, Larry Ploetz, Shanker Singh, April Wensel, Eva Huala
Database, Volume 2012, 2012, bas030, https://doi.org/10.1093/database/bas030
Published: 01 August 2012
Journal Article

CreZOO—the European virtual repository of Cre and other targeted conditional driver strains

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Christina Chandras, Michael Zouberakis, Ekaterina Salimova, Damian Smedley, Nadia Rosenthal, Vassilis Aidinis
Database, Volume 2012, 2012, bas029, https://doi.org/10.1093/database/bas029
Published: 21 June 2012
Journal Article

MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes

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Andreas Braun, Bettina Halwachs, Martina Geier, Katrin Weinhandl, Michael Guggemos, Jan Marienhagen, Anna J. Ruff, Ulrich Schwaneberg, Vincent Rabin, Daniel E. Torres Pazmiño, Gerhard G. Thallinger, Anton Glieder
Database, Volume 2012, 2012, bas028, https://doi.org/10.1093/database/bas028
Published: 21 June 2012